mem ismb 2009| Help | Intro | MEM - Multi Experiment Matrix
Enter gene ID(s) nanog (for example: Jun, 203325_s_at,
ENSG00000204531, ...) [?]
1 NANOG 1.1 1429388_AT (NANOG) Homeobox protein NANOG (Homeobox
transcription factor Nanog)(Early embryo specific expression
NK-type homeobox protein)(ES cell-associated protein 4)
Select collection A!ymetrix GeneChip® Mouse Genome 430 2.0
[Mouse430_2] (487 datasets) [?] Mouse
Submit query
Distance measure : pearson - Pearson correlation distance [?]
Rank aggregation method : Use betaMEM method to get p-value for
selected ranks [?]
Set score threshold : inf [?]
By default MEM displays most similar genes to QUERY, to invert this
action check: (and most distant genes will be
shown). [?]
[?] | GO annotations | ExpressView | URLMap link | Static URL |
Query details |Results
Handpicked datasets : : : : : reset all | 419 datasets excluded by
filters
[!]
E-GEOD-10806 Mouse iPS cells from neural stem cells by 2 factors
(Oct4, KLF4) (Kim, Zaehres et al.) [AE] E-GEOD-9563 Translation
state array analysis of Mouse embryonic stem cells and embryoid
bodies [AE] E-GEOD-10210 Gene expression analysis of embryonic stem
cells expressing VE-cadherin (CD144) during endothelial
differentiation [AE] E-GEOD-5671 Cardiac differentiation of
embryonic stem cells recapitulates embryonic cardiac development.
[AE] E-GEOD-4936 Transcriptional Profiling of Hh-Treated Embryoid
Bodies [AE] E-GEOD-5976 Mesp1-induced gene expression changes [AE]
E-GEOD-3463 Expression profiling of mouse gonadal somatic cells
[AE] E-GEOD-4308 Expression data for validation of single cell cDNA
amplification method (V1V3 method) [AE] E-GEOD-11128 Expression
data from single cells from mouse primordial germ cell lineage
(E6.25-E8.25, wild type and Blimp1KO) [AE] E-GEOD-6882 Embryonic
Ovary Developmental Time Course [AE] E-GEOD-9629 Comparison of
normal and beta catenin deficient kidney gene expression profiles
at E12.5 [AE] E-GEOD-6881 Embryonic Testis Developmental Time
Course [AE] E-GEOD-9760 Embryonic stem cells with expanded CAG
repeats (lorin-affy-mouse-501743) [AE] E-GEOD-4307 Expression data
from single cells from ICMs of mouse blastocysts at E3.5 [AE]
E-TABM-411 FlowResponse_W06 [AE] E-GEOD-11358 Histones associated
with downregulated genes are hypo-acetylated in HuntingtonâÂ!™s
disease models [AE] E-GEOD-11161 Gene expression profiles of
neonatal bladder samples. (GUDMAP Series_id: 19) [AE] E-GEOD-9247
Effect of histone deacetylase inhibitors on osteoblast gene
expression [AE] E-GEOD-13421 CBA/CaJ mouse cochlea gene expression
profile [AE] E-GEOD-7225 Identification and characterization of the
changed transcripts in cumulus cells of Bmp15-/- and
Bmp15-/-Gdf9+/--DM mice. [AE] E-GEOD-11040 Shared gene expression
profiles in developmental heart valve remodeling and osteoblast
progenitor cells [AE] E-GEOD-12694 Cooperative actions of p53 and
Pten in normal and neoplastic progenitor cell renewal and
differentiation [AE] E-GEOD-8828 Isolation and molecular
characterization of cancer stem cells in MMTVWnt-1 murine breast
tumors [AE] E-GEOD-6789 response to IL-1b of WT and IRAK4 kinase
dead mouse embryonic fibroblasts [AE] E-GEOD-6398 Comparison
between gene expression in heart from Lmna H222P homozygous and
control mice [AE] E-MIMR-42 EXP_EKMP_0504_01 [AE] E-GEOD-13235 Gene
expression profile of mouse embryonic stem cells (D3-pOCT-mESC)
grown in low concentrations of nitric oxide [AE] E-GEOD-7528 Gene
expression of Wt vs CYP26A1-/- murine ES cells treated with control
or 100 nM RA for 8 or 72 hr. [AE]
Dataset list (filtered out) [419 ds] [+]
Gene list [QUERY + 50 genes]
#Score #Gene name #probeset id #Gene description #QUERY NANOG
1429388_AT Homeobox protein NANOG (Homeobox transcription factor
Nanog)(Early embryo specific expression NK-type homeobox
protein)(ES cell-associated protein 4)
[Source:UniProtKB/Swiss-Prot;Acc:Q80Z64]
4.68e-26 POU5F1 1417945_at POU domain, class 5, transcription
factor 1 (Octamer-binding transcription factor
3)(Oct-3)(Oct-4)(NF-A3) [Source:UniProtKB/Swiss-Prot;Acc:P20263]
6.29e-25 ZFP42 1418362_at Zinc finger protein 42 (Zfp-42)(Reduced
expression protein 1)(REX-1)(mREX-1)
[Source:UniProtKB/Swiss-Prot;Acc:P22227] 2.23e-24 N/A 1457314_at
N/A 2.88e-24 DPPA2 1453223_s_at Developmental
pluripotency-associated protein 2 (Pluripotent embryonic stem
cell-related gene 1 protein)
[Source:UniProtKB/Swiss-Prot;Acc:Q9CWH0] 2.04e-22 RP24-335A2.3
1416552_at Developmental pluripotency-associated protein 5A
(mDppa5)(ES cell-associated transcript 2 protein)(Embryonal stem
cell-specific gene 1 protein)(Esg-1)(Protein pH 34)
[Source:UniProtKB/Swiss-Prot;Acc:Q9CQS7] 1.88e-21 ZIC3 1423424_at
Zinc finger protein ZIC 3 (Zinc finger protein of the cerebellum 3)
[Source:UniProtKB/Swiss-Prot;Acc:Q62521] 8.57e-21 SOX2 1416967_at
Transcription factor SOX-2 [Source:UniProtKB/Swiss-Prot;Acc:P48432]
2.02e-20 DPPA4 1429597_at Developmental pluripotency-associated
protein 4 [Source:UniProtKB/Swiss-Prot;Acc:Q8CCG4] 3.55e-20
RP23-353B17.1 1449064_at L-threonine 3-dehydrogenase, mitochondrial
Precursor (EC 1.1.1.103) [Source:UniProtKB/Swiss-Prot;Acc:Q8K3F7]
4.43e-19 EG435970 1443892_at hypothetical protein LOC435970
[Source:RefSeq peptide;Acc:NP_001030065] 9.43e-19 N/A 1454904_at
N/A 1.54e-18 DPPA3 1424295_at Developmental pluripotency-associated
protein 3 (Compaction-associated protein 1)(Primordial germ cell
protein 7) [Source:UniProtKB/Swiss-Prot;Acc:Q8QZY3] 1.62e-18 N/A
1434280_at N/A 2.17e-18 DPPA2 1429654_at Developmental
pluripotency-associated protein 2 (Pluripotent embryonic stem
cell-related gene 1 protein)
[Source:UniProtKB/Swiss-Prot;Acc:Q9CWH0] 1.03e-17 GDF3 1449288_at
Growth/differentiation factor 3 Precursor (GDF-3)(VG-1-related
protein 2) [Source:UniProtKB/Swiss-Prot;Acc:Q07104] 1.54e-17 MORC1
1419418_a_at MORC family CW-type zinc finger protein 1 (Protein
microrchidia) [Source:UniProtKB/Swiss-Prot;Acc:Q9WVL5] 2.83e-17 N/A
1434279_at N/A 3.61e-17 RP23-285N14.6 1438237_at reduced expression
2 [Source:RefSeq peptide;Acc:NP_033077] 3.92e-17 ZIC3 1438737_at
Zinc finger protein ZIC 3 (Zinc finger protein of the cerebellum 3)
[Source:UniProtKB/Swiss-Prot;Acc:Q62521] 4.22e-17 UTF1 1416899_at
Undifferentiated embryonic cell transcription factor 1
[Source:UniProtKB/Swiss-Prot;Acc:Q6J1H4] 6.22e-17 TCFAP2C
1436392_s_at Transcription factor AP-2 gamma (AP2-gamma)(Activating
enhancer-binding protein 2 gamma)(AP-2.2)
[Source:UniProtKB/Swiss-Prot;Acc:Q61312]
7e-17 SALL1 1437983_at Sal-like protein 1 (Zinc finger protein
Spalt-3)(Sal-3)(MSal-3) [Source:UniProtKB/Swiss-Prot;Acc:Q9ER74]
1.29e-16 PRDM14 1444390_at PR domain containing 14 [Source:RefSeq
peptide;Acc:NP_001074678] 1.58e-16 TDGF1 1450989_at
Teratocarcinoma-derived growth factor Precursor (Epidermal growth
factor-like Cripto protein)(Cripto growth factor)
[Source:UniProtKB/Swiss-Prot;Acc:P51865] 2.8e-16 SLC7A3 1417022_at
Cationic amino acid transporter 3 (CAT-3)(Cationic amino acid
transporter y+)(Solute carrier family 7 member 3)
[Source:UniProtKB/Swiss-Prot;Acc:P70423] 4.56e-16 FBXO15 1427238_at
F-box only protein 15 [Source:UniProtKB/Swiss-Prot;Acc:Q9QZN0]
5.07e-16 N/A 1444292_at N/A 1.38e-15 ZSCAN10 1438787_at zinc finger
and SCAN domains 10 [Source:RefSeq peptide;Acc:NP_001028597]
1.74e-15 TRIM6 1424448_at Tripartite motif-containing protein 6
[Source:UniProtKB/Swiss-Prot;Acc:Q8BGE7] 2.66e-15 LIPH 1457026_at
Lipase member H Precursor (EC 3.1.1.-)
[Source:UniProtKB/Swiss-Prot;Acc:Q8CIV3] 3.46e-15 RNF17 1438820_at
RING finger protein 17 (Mad member-interacting protein 2)(Mmip-2)
[Source:UniProtKB/Swiss-Prot;Acc:Q99MV7] 6.97e-15 ERAS 1456511_x_at
GTPase ERas Precursor (E-Ras)(Embryonic stem cell-expressed Ras)
[Source:UniProtKB/Swiss-Prot;Acc:Q7TN89] 7.85e-15 FGF4 1420085_at
Fibroblast growth factor 4 Precursor (FGF-4)(Heparin-binding growth
factor 4)(HBGF-4)(K-fibroblast growth factor)
[Source:UniProtKB/Swiss-Prot;Acc:P11403] 8.46e-15 NODAL 1422058_at
Nodal Precursor [Source:UniProtKB/Swiss-Prot;Acc:P43021] 1.14e-14
PHF17 1426752_at Protein Jade-1 (PHD finger protein 17)
[Source:UniProtKB/Swiss-Prot;Acc:Q6ZPI0] 1.22e-14 ESRRB 1436926_at
Steroid hormone receptor ERR2 (Estrogen-related receptor,
beta)(ERR-beta)(Estrogen receptor-like 2)(Nuclear receptor
subfamily 3 group B member 2)
[Source:UniProtKB/Swiss-Prot;Acc:Q61539] 1.56e-14 LRRC34 1429366_at
Leucine-rich repeat-containing protein 34
[Source:UniProtKB/Swiss-Prot;Acc:Q9DAM1] 1.91e-14 N/A 1434278_at
N/A 3.63e-14 DMRT1 1423582_at Doublesex- and mab-3-related
transcription factor 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9QZ59]
3.74e-14 TCFAP2C 1418147_at Transcription factor AP-2 gamma
(AP2-gamma)(Activating enhancer-binding protein 2 gamma)(AP-2.2)
[Source:UniProtKB/Swiss-Prot;Acc:Q61312] 4.73e-14 TGIF1
1422286_a_at Homeobox protein TGIF1 (5'-TG-3'-interacting factor 1)
[Source:UniProtKB/Swiss-Prot;Acc:P70284] 5.11e-14 2410003J06RIK
1429701_at Melanoma-associated antigen B16 (MAGE-B16 antigen)
[Source:UniProtKB/Swiss-Prot;Acc:Q9CWV4] 8.18e-14 FGF4 1420086_x_at
Fibroblast growth factor 4 Precursor (FGF-4)(Heparin-binding growth
factor 4)(HBGF-4)(K-fibroblast growth factor)
[Source:UniProtKB/Swiss-Prot;Acc:P11403] 9.21e-14 DND1 1455367_at
Dead end protein homolog 1 (RNA-binding motif,
single-stranded-interacting protein 4)
[Source:UniProtKB/Swiss-Prot;Acc:Q6VY05] 9.7e-14 N/A 1439065_x_at
N/A 1.68e-13 ZMYM1 1428052_a_at zinc finger, MYM domain containing
1 [Source:RefSeq peptide;Acc:NP_080946] 2.32e-13 EG653016
1456242_at Embryonic stem cell-and germ cell-specific protein ESGP
[Source:UniProtKB/TrEMBL;Acc:Q2Q5T5] 2.46e-13 DNMT3L 1425035_s_at
DNA (cytosine-5)-methyltransferase 3-like
[Source:UniProtKB/Swiss-Prot;Acc:Q9CWR8] 2.56e-13 TCL1 1422458_at
T-cell leukemia/lymphoma protein 1A (Protein p14 TCL1)(Oncogene
TCL1)(TCL-1) [Source:UniProtKB/Swiss-Prot;Acc:P56280]
2.65e-13 N/A 1456140_at N/A
Multi-Experiment-Matrix © 2008-2009 | Priit Adler & Jaak Vilo @
Biit Group, Institute of Computer Science, University of
Tartu
Thu Jun 11 12:32:09 2009 Thu Jun 11 12:32:28 2009 Duration : 0 m,
19 s CMD : 0 m, 14 s Output : 0 m, 3 s
Multi Experiment Matrix - web tool for mining co- expressed genes
over hundreds of datasets Priit Adlera, Raivo Koldebc, Meelis
Kullbc, Hedi Petersonac, Jüri Reimandb, Aleksandr Tkatšenkobc and
Jaak Vilobc
a Institute of Molecular and Cell Biology, University of Tartu, b
Institute of Computer Science, University of Tartu, c Quretec
Inc
biit.cs.ut.ee/mem
Abstract Accumulation of gene expression data in public domain has
raised the opportunity to discover new facts by re-analyzing
existing experiments. Co- expression over many gene expression
datasets has been proven useful in many areas of molecular biology
and bioinformatics, such as network reconstruction and gene
function prediction.
MEM query goes over hundreds of gene expression datasets from
ArrayExpress covering wide spectrum of biological conditions from
stem cells to different diseases and cancer. The essence of MEM is
a novel rank aggregation method that combines similarity searches
across individual data sets into a global ordering by selecting
automatically the appropriate experiments and assigning a combined
p-value for the significance of the similarity across all
data.
Conclusion We have developed a tool for finding co-expressed genes
over many public gene expression datasets. The tool has many
possible applications, such as gene function prediction or network
reconstruction. The search is powered by a novel rank aggregation
algorithm. User interface is highly interactive and provides
additional information about the query and the results.
Data From ArrayExpress database we have downloaded all AffyMetrix
GeneChip® gene expression datasets with raw data available.
Datasets are grouped by platform which makes features of
different
experiments easy to compare Many popular platforms have hundreds of
different experiments with
wide spectrum of conditions
Example of Collagen To illustrate the rank aggregation method
behind MEM query we used Collagen alpha-1(V) chain
Precursor(COL5A1) as an example. The rank distribution and dynamics
of p-value are depicted on the graph for fifth and 6250th result in
MEM query. For each gene we have a rank vector over all
datasets.
Ranks are sorted and for each rank a p-value is calculated to
measure how skewed towards the 0 it is.
Minima of the p-values is presented as MEM score.
Example of Nanog To emphasize the advantages of MEM, we observed
how many known targets1 of Nanog are found within top fifty. MEM
saves biologist's time by automating the selection of appropriate
datasets from large expression data collections.
Acknowledgements
This work has been supported by EU FP6 ENFIN, FunGenES, Estonian
Science Foundation 5724, 7437 Priit Adler has been awarded a Travel
Fellowship by ISMB/ECCB 2009 to present this poster.
1 Sharov, Alexei and Masui, Shinji and Sharova, Lioudmila and Piao,
Yulan and Aiba, Kazuhiro and Matoba, Ryo and Xin, Li and Niwa,
Hitoshi and Ko, Minoru. Identification of Pou5f1, Sox2, and Nanog
downstream target genes with statistical confidence by applying a
novel algorithm to time course microarray and genome-wide chromatin
immunoprecipitation data. BMC Genomics, vol 9, 2008
Method
Query gene by user In each dataset genes are sorted according to a
query gene
The distance measure used in this step can be arbitrary
The results are converted into ranks Overall we get a rank matrix
and for each
gene we end up a rank vector over all datasets
We expect two different distributions from rank vector:
• uniform if there is no connection between genes (e.g. Collagens
6250th neighbour)
• skewed towards 0 if genes are co-expressed (e.g. Collagens 5th
neighbour)
Ranks are aggregated into p-values With the p-value measures
deviation from
uniform distribution. More small ranks leads to smaller
p-value.
MEM result Individual datasets StDev 0.29 threshold